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- PDB-9iby: Crystal structure of Zika Virus NS2B-NS3 protease in complex with... -

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Basic information

Entry
Database: PDB / ID: 9iby
TitleCrystal structure of Zika Virus NS2B-NS3 protease in complex with compound 2
ComponentsGenome polyprotein
KeywordsHYDROLASE / Zika virus / NS2B-NS3 Protease / allosteric inhibitor / compound 1
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / molecular adaptor activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / molecular adaptor activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / lipid binding / symbiont entry into host cell / GTP binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / ACETIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.291 Å
AuthorsOntario, J.M. / Torrente, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Zika Virus NS2B-NS3 protease in complex with compounds to be submitted
Authors: Ontoria, J.M. / Torrente, E.
History
DepositionFeb 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8277
Polymers48,7062
Non-polymers1,1215
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-7 kcal/mol
Surface area16940 Å2
Unit cell
Length a, b, c (Å)61.793, 57.472, 72.447
Angle α, β, γ (deg.)90.000, 96.406, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 50 - 1155 / Label seq-ID: 6 - 215

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Genome polyprotein


Mass: 24353.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A140DLX4
#2: Chemical ChemComp-A1I16 / 1-[3-[[5-(4,6-dimethylpyrimidin-5-yl)pyridin-2-yl]methyl]-1-oxa-2,3$l^{4}-diazacyclopenta-2,4-dien-5-yl]-3-[3-(trifluoromethyl)phenyl]urea


Mass: 470.427 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H19F3N7O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: 12.00 %w/v PEG 8K 20.00 %v/v Glycerol 0.16 M Mg Acet 0.08 M Na Cacod
PH range: 6.25-6.75

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jan 24, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.291→44.961 Å / Num. obs: 14363 / % possible obs: 89.6 % / Redundancy: 6.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.141 / Net I/σ(I): 6.8
Reflection shellResolution: 2.291→2.581 Å / Rmerge(I) obs: 1.53 / Num. unique obs: 718 / CC1/2: 0.508

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
autoPROCdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.291→44.956 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.412 / SU ML: 0.203 / Cross valid method: FREE R-VALUE / ESU R: 0.433 / ESU R Free: 0.276
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2357 733 5.103 %
Rwork0.189 13630 -
all0.191 --
obs-14363 62.617 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.785 Å2
Baniso -1Baniso -2Baniso -3
1-0.091 Å2-0 Å2-0.593 Å2
2--0.386 Å20 Å2
3----0.335 Å2
Refinement stepCycle: LAST / Resolution: 2.291→44.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2462 0 80 54 2596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0122522
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162287
X-RAY DIFFRACTIONr_ext_dist_refined_b0.0150.053
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.8183443
X-RAY DIFFRACTIONr_angle_other_deg0.5131.7455217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0225324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.1731018
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32810318
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.1910.61997
X-RAY DIFFRACTIONr_dihedral_angle_other_6_deg18.356204
X-RAY DIFFRACTIONr_chiral_restr0.0660.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023048
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02560
X-RAY DIFFRACTIONr_nbd_refined0.1710.2366
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.22049
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21180
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21253
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0070.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1020.26
X-RAY DIFFRACTIONr_nbd_other0.1530.236
X-RAY DIFFRACTIONr_mcbond_it2.9525.3091305
X-RAY DIFFRACTIONr_mcbond_other2.9535.3041302
X-RAY DIFFRACTIONr_mcangle_it5.0419.5091624
X-RAY DIFFRACTIONr_mcangle_other5.049.5141625
X-RAY DIFFRACTIONr_scbond_it2.8915.1781217
X-RAY DIFFRACTIONr_scbond_other2.895.181218
X-RAY DIFFRACTIONr_scangle_it4.8069.4981819
X-RAY DIFFRACTIONr_scangle_other4.8049.4991820
X-RAY DIFFRACTIONr_lrange_it7.45248.072582
X-RAY DIFFRACTIONr_lrange_other7.44548.0832578
X-RAY DIFFRACTIONr_ncsr_local_group_10.0340.051662
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.033540.05
12BX-RAY DIFFRACTIONLocal ncs0.033540.05
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.291-2.350.27130X-RAY DIFFRACTION
2.35-2.4140.29750.373102X-RAY DIFFRACTION6.5564
2.414-2.4840.41770.32181X-RAY DIFFRACTION11.75
2.484-2.560.323230.308272X-RAY DIFFRACTION18.9467
2.56-2.6440.32280.316507X-RAY DIFFRACTION35.9543
2.644-2.7360.402330.33605X-RAY DIFFRACTION43.7886
2.736-2.8390.34430.274910X-RAY DIFFRACTION69.108
2.839-2.9550.258560.2541049X-RAY DIFFRACTION80.5394
2.955-3.0850.266790.2541144X-RAY DIFFRACTION94.5131
3.085-3.2350.267470.2151203X-RAY DIFFRACTION100
3.235-3.4090.215730.2061100X-RAY DIFFRACTION100
3.409-3.6150.272600.19971X-RAY DIFFRACTION91.3197
3.615-3.8630.256390.169971X-RAY DIFFRACTION95.8254
3.863-4.170.219500.148886X-RAY DIFFRACTION95.5102
4.17-4.5640.172370.132869X-RAY DIFFRACTION100
4.564-5.0960.148490.132782X-RAY DIFFRACTION99.7599
5.096-5.8720.22280.171701X-RAY DIFFRACTION100
5.872-7.1610.264280.192609X-RAY DIFFRACTION100
7.161-10.0010.175280.184459X-RAY DIFFRACTION100
10.001-44.9560.335200.246279X-RAY DIFFRACTION100

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